title: Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes.
abstract: OBJECTIVE
  Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC will enable identification of molecular subtypes and provide potential targets for early detection and therapy.
  
  
  METHODS
  We followed up a previous array study with additional discovery and confirmatory studies in new ESCC cases by using alternative methods. We profiled global gene expression for discovery and confirmation, and validated selected dysregulated genes with additional RNA and protein studies.
  
  
  RESULTS
  A total of 159 genes showed differences with extreme statistical significance (P < E-15) and 2-fold differences or more in magnitude (tumor/normal RNA expression ratio, N = 53 cases), including 116 upregulated and 43 downregulated genes. Of 41 genes dysregulated in our prior array study, all but one showed the same fold change directional pattern in new array studies, including 29 with 2-fold changes or more. Alternative RNA expression methods validated array results: more than two thirds of 51 new cases examined by real-time PCR (RT-PCR) showed 2-fold differences or more for all seven genes assessed. Immunohistochemical protein expression results in 275 cases which were concordant with RNA for five of six genes.
  
  
  CONCLUSIONS
  We identified an expanded panel of genes dysregulated in ESCC and confirmed previously identified differentially expressed genes. Microarray-based gene expression results were confirmed by RT-PCR and protein expression studies. These dysregulated genes will facilitate molecular categorization of tumor subtypes and identification of their risk factors, and serve as potential targets for early detection, outcome prediction, and therapy.
authors.affiliation: Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Su
authors.forename: Nan
authors.initials: N
authors.lastname: Hu
authors.forename: Howard H
authors.initials: HH
authors.lastname: Yang
authors.forename: Chaoyu
authors.initials: C
authors.lastname: Wang
authors.forename: Mikiko
authors.initials: M
authors.lastname: Takikita
authors.forename: Quan-Hong
authors.initials: QH
authors.lastname: Wang
authors.forename: Carol
authors.initials: C
authors.lastname: Giffen
authors.forename: Robert
authors.initials: R
authors.lastname: Clifford
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Hewitt
authors.forename: Jian-Zhong
authors.initials: JZ
authors.lastname: Shou
authors.forename: Alisa M
authors.initials: AM
authors.lastname: Goldstein
authors.forename: Maxwell P
authors.initials: MP
authors.lastname: Lee
authors.forename: Philip R
authors.initials: PR
authors.lastname: Taylor
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000175:diagnosis* / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D004938:Esophageal Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D046228:Microarray Analysis; D042282:Microdissection; D008875:Middle Aged; D010641:Phenotype; D011379:Prognosis